Re: [R-sig-phylo] chronos ape substitution rate strict clock

2024-03-04 Thread Klaus Schliep
Dear Vincenzo, For ML estimates the edge length are the expected number of substitutions per site, which depends on the product of rate and time. So you need either a rate estimate or calibration points to estimate the time. If you divide the edge length by the rate the edges should be proportio

Re: [R-sig-phylo] Parallelization in ape::dist.topo

2023-03-07 Thread Klaus Schliep
__ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Senior Scientist Institute of Molecular Biotechnology TU Graz https://www

Re: [R-sig-phylo] ancestral state reconstruction with a complex discrete, trait

2022-11-16 Thread Klaus Schliep
___ > > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > [[alternative HTML version deleted]] > > ___________ > R

Re: [R-sig-phylo] dist.nodes

2021-09-07 Thread Klaus Schliep
-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-pr

Re: [R-sig-phylo] Using bind.tip and lapply on a multiPhylo object

2021-06-03 Thread Klaus Schliep
taxon? I've noticed adding a 'mrca' > argument also increases computation time and if I am reinventing the wheel > it would be nice to know if I am overthinking things. > > Sincerely, > Russell > > [[alternative HTML version deleted]] > > ______

Re: [R-sig-phylo] phangorn

2021-04-06 Thread Klaus Schliep
tp://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Senior Scientist Institute of Computational Biotechnology TU Graz https://icbt.tugraz.at https://www.phangorn.org/ <http://www.phangorn.org/> [[alternative HTML version deleted]]

Re: [R-sig-phylo] extracting sister taxon pairs from phylo object in APE R package

2020-01-10 Thread Klaus Schliep
> ___ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > > https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&

Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package

2018-06-08 Thread Klaus Schliep
Hi Sebastian, there is an implementation of the SH-test and SOWH-test in phangorn. Send me an mail off list if you have problems using them. Regards, Klaus On Jun 8, 2018 8:50 AM, "Sebastian Y. Müller" wrote: Dear all, I'd was wondering how to best perform a test to determine test disagreement

Re: [R-sig-phylo] importing trees from birdtree.org into R

2018-02-13 Thread Klaus Schliep
1, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

2017-12-15 Thread Klaus Schliep
http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org R-sig-phylo@r-project.org> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/

Re: [R-sig-phylo] Possible Bug in ape::read.tree

2017-09-05 Thread Klaus Schliep
(R 3.4.1) >>> parallel 3.4.1 2017-06-30 local >>> prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.1) >>> progress 1.1.2 2016-12-14 CRAN (R 3.4.1) >>> R62.2.2 2017-06-17 CRAN (R 3.4.0) >>> Rcpp 0.12.12 2017-07-15

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

2017-07-26 Thread Klaus Schliep
g list - R-sig-phylo@r-project.org > > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > Searchable archive at http://www.mail-archive.com/r- > > > sig-ph...@r-project.org/ > > > > > > > [[alternative HTML version deleted]] > > > > > > > >

Re: [R-sig-phylo] A possible alternate MRCA function to APE's getMRCA

2017-06-10 Thread Klaus Schliep
turn(NULL) >>>Ntip <- length(phy$tip.label) >>>rootnd <- Ntip + 1L >>> >>>pars <- integer(phy$Nnode) # worst case assignment, usually far too >>> long >>>mrcaind <- 1L # index in pars of the mrca node. will return highest >>&

Re: [R-sig-phylo] A possible alternate MRCA function to APE\'s getMRCA

2017-06-09 Thread Klaus Schliep
> >>> <https://www.avast.com/sig-email?utm_medium=email&utm_ > source=link&utm_campaign=sig-email&utm_content=emailclient> > >>> > >>> > >>> > >>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > >>> &g

Re: [R-sig-phylo] A possible alternate MRCA function to APE's getMRCA

2017-06-07 Thread Klaus Schliep
tnd); > } > idx <- which(pars == cpar); > if (idx > mrcaind) { > mrcaind <- idx; > } > done <- TRUE; > } else { > # keep going! > cnd

Re: [R-sig-phylo] Graphically comparing multiple trees

2017-04-27 Thread Klaus Schliep
mated way to do it. > > >> :-) > > >> Sincerely, > > >> V. > -- > Vojtěch Zeisek > https://trapa.cz/en/ > > Department of Botany, Faculty of Science > Charles University, Prague, Czech Republic > https://www.natur.cuni.cz/biology/botany/ > > Institute

Re: [R-sig-phylo] Graphically comparing multiple trees

2017-04-25 Thread Klaus Schliep
ttp://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> >> > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-ar

Re: [R-sig-phylo] distances between the nodes

2017-03-01 Thread Klaus Schliep
rzbin...@dkfz-heidelberg.de> wrote: > Dear Klaus, > > > > Thanks a lot for your help > > > > and what is in that case xx and yy? > > > > Justyna > > > > *From:* Klaus Schliep [mailto:klaus.schl...@gmail.com] > *Sent:* Friday, February 24, 2017 6:13 PM

Re: [R-sig-phylo] distances between the nodes

2017-02-24 Thread Klaus Schliep
Josef Puchta >> >> VAT-ID No.: DE143293537 >> >> >> >> ___ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at http:/

Re: [R-sig-phylo] HKY GTR distances

2017-02-07 Thread Klaus Schliep
rtment of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >

Re: [R-sig-phylo] Enigmatic error with drop.tip

2017-01-20 Thread Klaus Schliep
________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell La

Re: [R-sig-phylo] multi2di fails on multiPhylo objects

2017-01-13 Thread Klaus Schliep
mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/

Re: [R-sig-phylo] phylo from igraph

2017-01-06 Thread Klaus Schliep
ncouver, Canada > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ >

Re: [R-sig-phylo] Extract all possible clades from a tree

2017-01-05 Thread Klaus Schliep
I had a look at the tree. There seems a bug in extract.clades, when the tree was rooted before with the root() function. extract.clade() seem to expect some ordering of nodes which seems not satisfied (and it looks as it was written a long time ago). I just wrote a small function (easier than to d

Re: [R-sig-phylo] Midpoint root a tree with root() function ape ver 4.0

2016-12-15 Thread Klaus Schliep
___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University

Re: [R-sig-phylo] compressTipLabel as an option to read.trees()

2016-12-14 Thread Klaus Schliep
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/ [[alternative HTML version delete

Re: [R-sig-phylo] concatenating loci with different taxa

2016-11-18 Thread Klaus Schliep
g > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/ [[alternative HTML versio

Re: [R-sig-phylo] Making ultrametric trees

2016-10-31 Thread Klaus Schliep
>><https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> > >>>><https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >><https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>> > >>>>> Searchable archive at > >&g

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

2016-09-12 Thread Klaus Schliep
Dear Rav, write.dna() from ape just does this. Klaus On Sep 12, 2016 9:07 AM, "Bhuller, Ravneet" < ravneet.bhulle...@imperial.ac.uk> wrote: > Hi Thibaut, > > Is there anyway I can save the concatenated alignment (created using apex > and the concatenate function) in FASTA format? > > Regards, > >

Re: [R-sig-phylo] Ultrametric tree not recognized

2016-08-19 Thread Klaus Schliep
> > option = 1 => using the criterion you suggested below > option = 2 => using the current 'variance' criterion > > And other criteria could be added. > > What do you think? > > Best, > > Emmanuel > > > Le 17/08/2016 à 19:16, Klaus Schliep a

Re: [R-sig-phylo] Ultrametric tree not recognized

2016-08-17 Thread Klaus Schliep
ultrametric(phy, tol = .Machine$double.eps^0.5). > According to ?.Machine this value does not depend on the machine precision. > On my laptop, it gives: > > R> .Machine$double.eps^0.5 > [1] 1.490116e-08 > > Best, > > Emmanuel > > > Le 16/08/2016 à 18:15,

Re: [R-sig-phylo] Ultrametric tree not recognized

2016-08-16 Thread Klaus Schliep
tionary Biology > Room 2071, Kraus Natural Sciences Building > Ann Arbor MI 48109-1079 > josep...@umich.edu > > > > On 16 Aug, 2016, at 10:15, Klaus Schliep wrote: > > Hello all, > this may come be surprising to many, but consulting the manual > ?is.ultrametric can be

Re: [R-sig-phylo] Ultrametric tree not recognized

2016-08-16 Thread Klaus Schliep
Hello all, this may come be surprising to many, but consulting the manual ?is.ultrametric can be helpful. Why not simply try e.g. is.ultrametric(tree, tol=.01) So in this sense RTFM Regards, Klaus On Aug 16, 2016 9:31 AM, "Martin Dohrmann" wrote: > > Am 16.08.2016 um 15:20 schrieb Joseph W.

[R-sig-phylo] Nantucket phylogeny developeR bootcamp

2016-06-19 Thread Klaus Schliep
f the workshop, course leaders Drs. April Wright and Klaus Schliep (with Dr. Liam Revell participating remotely) will provide an introduction to the primary data structures and methods of common phylogenetic R packages, the basics of computational algorithms for phylogenies, and an overview of pa

Re: [R-sig-phylo] Error in plotBS when number of taxa is small

2016-06-14 Thread Klaus Schliep
HI Kamilla, can you send me your code and data and what phangorn version are you using? Cheers, Klaus On Tue, Jun 14, 2016 at 6:42 PM, Kamila Naxerova wrote: > Hi all, > > I am trying to attach bootstrap values to a small tree (just 4 taxa). > plotBS() in the phangorn package gives me the follow

Re: [R-sig-phylo] new testing version of ape

2016-02-22 Thread Klaus Schliep
> > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > > [[alternative HTML version deleted

Re: [R-sig-phylo] colouring tree branches like tips

2016-01-26 Thread Klaus Schliep
t; PhD candidate > > Wageningen University > Laboratory of Biochemistry > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > Phone 31 317483387 > e-mail: gudrun.gy...@wur.nl > > - - - - - - - - - - - - - - - - - - > > Project information: > http://www.wagening

Re: [R-sig-phylo] colouring tree branches like tips

2016-01-26 Thread Klaus Schliep
; G > > > > Gudrun Gygli, MSc > > PhD candidate > > Wageningen University > Laboratory of Biochemistry > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > Phone 31 317483387 > e-mail: gudrun.gy...@wur.nl > > - - - - - - - - - - - - - - - - -

Re: [R-sig-phylo] extract parent-child from newick

2016-01-12 Thread Klaus Schliep
710 > Cell 423-676-7489 > Office/lab 423-439-4359 > Fax423-439-5958 > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.

Re: [R-sig-phylo] Package phytools load failed

2016-01-09 Thread Klaus Schliep
Hi all, you have to install the Biostrings package from bioconductor. Than it should works. Phangorn has a dependency on biostrings and phytools depend on phangorn. Have a nice weekend Klaus Am 09.01.2016 16:35 schrieb "Donald Miles" : > Dear All, > > I receive the same error as Gabriela when I tr

Re: [R-sig-phylo] Calculating branch lengths on a multiphylo object

2016-01-01 Thread Klaus Schliep
s,foo) > Error in lapply(ttrees, foo) : object 'ttrees' not found > > class(trees)<-"multiPhylo" > > fit.equal<-t(mapply(fit.model,trees,xy)) > Error in mapply(fit.model, trees, xy) : object 'xy' not found > > mean(fit.equal[,1]) ## should

Re: [R-sig-phylo] Detecting homoplasy

2015-12-18 Thread Klaus Schliep
Dear Tim, I added an optional argument sitewise to the CI and RI function in phangorn. The vector may contains NaN if the function is undefined: pscore of 0 for CI, uninformative site for RI. It is now on github: library(devtools) install_github("KlausVigo/phangorn") Cheers, Klaus On Thu, Dec 1

[R-sig-phylo] Problems with dependency Biostrings

2015-12-17 Thread Klaus Schliep
lled any bioconductor packages, chances are that you also installed Biostrings package are pretty high. Regards, Klaus -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted]] __

Re: [R-sig-phylo] Mapping gene gain loss info to rooted species tree

2015-11-16 Thread Klaus Schliep
http://www.linkedin.com/in/anandksrao> > _ > CTTATTGTTGAACTTOAATGGTGCTAATGATCCTCGTOTCTCCTGAACGT - translate THAT! > > [[alternative HTML version deleted]] > > ________

Re: [R-sig-phylo] dist.nodes crashing with big trees

2015-10-20 Thread Klaus Schliep
That's fine with me. On Tue, Oct 20, 2015 at 3:29 PM, David Bapst wrote: > Ah, thanks, Klaus! I was is it alright with you if I merge these edits > into paleotree? > -Dave > > On Tue, Oct 20, 2015 at 1:15 PM, Klaus Schliep > wrote: > > Hi Gustavo & Davi

Re: [R-sig-phylo] dist.nodes crashing with big trees

2015-10-20 Thread Klaus Schliep
Best, > > *Gustavo Burin Ferreira, **Msc.* > Instituto de Biociências > Universidade de São Paulo > Tel: (11) 98525-8948 > > On Tue, Oct 20, 2015 at 5:15 PM, Klaus Schliep > wrote: > >> Hi Gustavo & David, >> >> I attached a file that contains a

Re: [R-sig-phylo] dist.nodes crashing with big trees

2015-10-20 Thread Klaus Schliep
t; > > Searchable archive at > > > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > > > > > > > > > > > -- > > > David W. Bapst, PhD > > > Adjunct Asst. Professor, Geology and Geol. Eng. > > > South Dakota Schoo

Re: [R-sig-phylo] issue in ape's rphylo (and workaround)

2015-10-04 Thread Klaus Schliep
1.0135 > > write.tree(phy=ltr, file="") > [1] > > "((t2:0.06701971429,t1:0.06701971429):2.686176768,(t5:1.207768321,(t6:0.4984853178,(t4:1.013489985,t3:1.013489985):0.09146602338):0.1028123128):1.545428161);" > > > > tr_wFossils = read.tree(file=""

Re: [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize?

2015-10-04 Thread Klaus Schliep
~--~--~--- > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archi

Re: [R-sig-phylo] Plotting rooted tree with bootstrap values (ape/phangorn)

2015-08-31 Thread Klaus Schliep
Dear Kamila, plotBS checks if trees are rooted or not and if not midpoint roots the tree nrooted <- root(nj(dist),outgroup=x) is.rooted(nrooted) # returns FALSE however the ape function does not pick up that the tree is rooted. Add the argument resolve.root=TRUE: nrooted <- root(nj(dist),outgroup=

Re: [R-sig-phylo] Cannot plot above 500 superimposed trees with densiTree (Phangorn)

2015-08-25 Thread Klaus Schliep
leX = FALSE, col = 1, width = 1, cex = 0.8) > > > (THIS DOES NOT WORK!) > > > Thanks in advance for helping me with this! > > > Marina > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-si

Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type="fan"

2015-07-30 Thread Klaus Schliep
TML version deleted]] > > _______ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus

Re: [R-sig-phylo] Prune very large tree

2015-07-15 Thread Klaus Schliep
.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted]] __

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

2015-06-12 Thread Klaus Schliep
t; > http://webpages.sdsmt.edu/~dbapst/ > http://cran.r-project.org/web/packages/paleotree/index.html > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at >

Re: [R-sig-phylo] Phylogenetic analysis with sequencing error

2015-01-23 Thread Klaus Schliep
ng that something like pml (phangorn) can be modified to do > that, but I haven't been able to figure it out myself yet. > > Thanks in advance, > George > > [[alternative HTML version deleted]] > > _______ > R-sig-phylo m

Re: [R-sig-phylo] Problem loading phytools on Mac

2014-12-22 Thread Klaus Schliep
using phytools on a PC. Anybody > know what gives here? > > cheers, > > Gabe > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http

Re: [R-sig-phylo] phangorn - midpoint function

2014-11-21 Thread Klaus Schliep
list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML vers

Re: [R-sig-phylo] Identify nodes along a pathway from root to a given tip

2014-11-04 Thread Klaus Schliep
Hello Manabu, try Ancestors from phangorn. Regards Klaus Am 04.11.2014 08:12 schrieb "Manabu Sakamoto" : > Dear list, > > I was wondering if there was an existing function to identify all the nodes > (e.g., phylo$edge[,1]) along a pathway from the root to any given tip. > > I've found Descendants

Re: [R-sig-phylo] Network from gene trees

2014-11-03 Thread Klaus Schliep
Hello Vojt�ch, have you looked into consensusNet in phangorn? Regards, Klaus Am 03.11.2014 03:10 schrieb "Vojt�ch Zeisek" : > Hello, > let's say I have many gene trees (all have same labels) in one multiPhylo > object. The trees are not fully congruent. One of the reasons can be > hybridization

Re: [R-sig-phylo] sitewise parsimony scores with parsimony()

2014-10-30 Thread Klaus Schliep
gt; [1] 2 1 1 > > There are four positions (X1-X4) but only three site patterns and > therefore three parsimony scores. > > Thank you. > > Rob > > > > > > [[alternative HTML version deleted]] > > ___ > R-sig-phyl

Re: [R-sig-phylo] Extracting sister groups

2014-10-23 Thread Klaus Schliep
absence of the trait, and ideally is capable >> of generating a dataframe of the appropriate format for the above functions >> automatically. It seems that a function to do this should exist already, >> but as I can't seem to find anything I would appreciate some help >>

Re: [R-sig-phylo] midpoint rooting? how to get the outgroup?

2014-10-23 Thread Klaus Schliep
gt; />/ Thanks, > />/ > />/ Robin > />/ > />/ Robin van Velzen > />/ PhD student > />/ Biosystematics Group > />/ Wageningen University > />/ > />/ Wageningen Campus, Radix building 107, Room W4.Aa.095 > />/ Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands &

Re: [R-sig-phylo] tip order in phylogeny - How does it work?

2014-10-09 Thread Klaus Schliep
"S28" > >> "S18" "S5""S11" "S18.1" "S20.1" "S16.1" > > > >> When I plot any tree in treeP, S18.1, S20.1 and S16.1 appear together > with > >> S18, S20 and S16, as intended. So why are t

Re: [R-sig-phylo] Plotting Posterior Probabilities from MrBayes Trees (An Update)

2014-10-08 Thread Klaus Schliep
correct tree and the OutbreakTools function > >> is not. We can see the why with last three lines in the console: > >> > >> identical(tree1$tip.label,tree2$tip.label) > >> > >> [1] TRUE > >> > >> identical(tree1$edge.length,tree2$edge.length) &g

Re: [R-sig-phylo] Why "dist.nodes" do no work if I use long tree?

2014-07-08 Thread Klaus Schliep
392:195)),(A393:198,(A394:269,(A395:97,A396:184) > > )),((A397:18,(A398:281,(A399:343,(A400:238,A401:280,(A402:163,(A403:308, > > ((A404:399,(A405:317,(A406:40,A407:191))),(((A408:230,A409:350),(A410:112,(A > > 411:346,(A412:68,(A413:387,(A414:332,A415:333)),(A416:250,(A417:232,(A41 > > 8:348,(A419:67,(

Re: [R-sig-phylo] (no subject)

2014-06-03 Thread Klaus Schliep
ystématique et Evolution Case postale 39 > UMR CNRS 7205 > > 57 rue cuvier > > FRANCE-75005 Paris > > portable +33629375132 > poste 0140793200 > > [[alternative HTML version deleted]] > > > ___ > R-sig-ph

Re: [R-sig-phylo] "Ape" package.

2014-04-20 Thread Klaus Schliep
-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep [[alternative HTML version deleted]] ___ R-sig-phylo mailing l

Re: [R-sig-phylo] Fatal Crash in ancestral.pars in phangorn

2014-04-08 Thread Klaus Schliep
ls=sort(unique(char))) > > anc<-ancestral.pars(tree,char,type="MPR") #here's the crash! > > > > -- > David W. Bapst, PhD > Adjunct Asst. Professor, Geology and Geol. Eng. > South Dakota School of Mines and Te

Re: [R-sig-phylo] chronos and gammaStat

2014-04-08 Thread Klaus Schliep
this is the problem? > Should I convert it? > > Thanks! > > ------ > *De:* Klaus Schliep > *Para:* Fabricia Nascimento > *Cc:* "r-sig-phylo@r-project.org" > *Enviadas:* Terça-feira, 8 de Abril de 2014 13:20 > > *Assunto:* Re: [R-sig-ph

Re: [R-sig-phylo] chronos and gammaStat

2014-04-08 Thread Klaus Schliep
> > Thanks! > Fabricia. > > ---------- > *De:* Klaus Schliep > *Para:* Fabricia Nascimento > *Cc:* "r-sig-phylo@r-project.org" > *Enviadas:* Terça-feira, 8 de Abril de 2014 13:13 > *Assunto:* Re: [R-sig-phylo] chronos and gammaStat > > Hello Frabricia, &

Re: [R-sig-phylo] chronos and gammaStat

2014-04-08 Thread Klaus Schliep
gt; > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep [[alter

Re: [R-sig-phylo] Help with plot.phylo, how to extract the tips points coordinates and how to controle de plot area.

2014-03-19 Thread Klaus Schliep
lor="black", > edge.width=3,add=T) > > -- > Grato > Augusto C. A. Ribas > > Site Pessoal: http://recologia.com.br/ <http://augustoribas.heliohost.org> > Github: https://github.com/Squiercg > Lattes: http://lattes.cnpq.br/7355685961127056 > > [[alter

Re: [R-sig-phylo] Generate all possible trees for n species

2014-03-08 Thread Klaus Schliep
his how to predict the number of possible trees? > > Best Wishes, Augusto Ribas > > -- > Grato > Augusto C. A. Ribas > > Site Pessoal: http://recologia.com.br/ <http://augustoribas.heliohost.org> > Github: https://github.com/Squiercg > Lattes: http://lattes.c

Re: [R-sig-phylo] Midpoint rooting routine?

2014-02-02 Thread Klaus Schliep
ctive and >> has two levels of menus. >> >> Joe >> >> Joe Felsenstein j...@gs.washington.edu >> Department of Genome Sciences and Department of Biology, >> University of Washington, Box 355065, Seattle, WA 98195-5065 USA >> > > ___

Re: [R-sig-phylo] Run time for pglmm.fit in picante

2013-09-06 Thread Klaus Schliep
or ways I could modify the pglmm.fit function to > speed the estimation process? > > Thanks in advance for any suggestions. And thanks to Tony and Matt for > developing these models and making them available in R. > > Dan > > ______

Re: [R-sig-phylo] compar.gee crashing R

2013-08-24 Thread Klaus Schliep
; > Thank you & cheers, > Sereina > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus

[R-sig-phylo] Fwd: Collapsing branches with low bootstrap values

2013-08-22 Thread Klaus Schliep
-- Forwarded message -- From: Klaus Schliep Date: Thu, Aug 22, 2013 at 6:12 PM Subject: Re: [R-sig-phylo] Collapsing branches with low bootstrap values To: "Naxerova, Kamila" Hi Kamila, try function pruneTree in phangorn. data(woodmouse) f <- function(x) nj(di

Re: [R-sig-phylo] Collapsing branches with low bootstrap values

2013-08-22 Thread Klaus Schliep
___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Phylogenomics Lab at the University of V

Re: [R-sig-phylo] getting a list of clusters with their associated bootstrap support

2013-06-11 Thread Klaus Schliep
! > > Douda > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ >

Re: [R-sig-phylo] Incongruence

2013-05-20 Thread Klaus Schliep
tinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ [[alternative HTML version deleted]] __

Re: [R-sig-phylo] Find common ancestor of multiple taxa

2013-05-09 Thread Klaus Schliep
R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> > > ___________ > R-sig-phylo mailing list - R-sig-phylo

Re: [R-sig-phylo] Very simple question on fitted values and scatterplots

2013-05-02 Thread Klaus Schliep
r Cell Biology and Genetics* > * > (MPI-CBG) > * > * > Pfotenhauerstraße 108 > * > * > 01307 Dresden > * > * > > * > * > Phone: +49 351 210-2621 > * > *Mail: prudent [ at ] mpi-cbg.de > **---* > > [[alt

Re: [R-sig-phylo] dist.dna -- inconsistent behavior with ambiguous sequences

2013-05-02 Thread Klaus Schliep
> Joe Felsenstein j...@gs.washington.edu > Department of Genome Sciences and Department of Biology, > University of Washington, Box 355065, Seattle, WA 98195-5065 USA > > > > > [[alternative HTML version deleted]] > > ___

Re: [R-sig-phylo] degrees of freedom issue in pgls() 'caper'

2013-04-23 Thread Klaus Schliep
rong! > > > Any input welcome, > > cheers, > Xavier > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http:/

Re: [R-sig-phylo] read.nexus.data parser

2013-04-09 Thread Klaus Schliep
ject.org/ >> > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus S

Re: [R-sig-phylo] Fwd: error in pruning tree

2013-04-05 Thread Klaus Schliep
bel, ] > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-pro

Re: [R-sig-phylo] problem with drop.tip

2013-02-28 Thread Klaus Schliep
ltiPhylo" plot(tr2) for(i in 1:1000){print(i);write.tree(tr2[[i]])} # may helps find you the trees which fail write.tree(tr2, file="result.tre") Cheers, Klaus On 2/28/13, Klaus Schliep wrote: > Dear John, > > can you please be a bit more specific with your error message.

Re: [R-sig-phylo] problem with drop.tip

2013-02-28 Thread Klaus Schliep
sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phyl

Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?

2013-02-19 Thread Klaus Schliep
s://www.researchgate.net/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info > > [[alternative HTML version deleted]] > > -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https

Re: [R-sig-phylo] From ClustalW2 Tree to Heat Map in R

2013-01-10 Thread Klaus Schliep
@helmholtz-hzi.de> > > > > > Helmholtz-Zentrum f?r Infektionsforschung GmbH | Inhoffenstra?e 7 | 38124 > Braunschweig | www.helmholtz-hzi.de > > Vorsitzende des Aufsichtsrates: MinDir'in B?rbel Brumme-Bothe, > Bundesministerium f?r Bildung

Re: [R-sig-phylo] issue with cophenetic.phylo()

2012-12-07 Thread Klaus Schliep
[1] -2.220446e-16 > > I am posting this in case it is of interest to others. As a quick fix, > I am now rounding x. > > Thanks, > Kelly > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list -

Re: [R-sig-phylo] estimating mutation rates

2012-11-09 Thread Klaus Schliep
>>> > R-sig-phylo mailing list >>> > R-sig-phylo@r-project.org >>> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> > >>> >>> [[alternative HTML version deleted]] >>> >>> >>> __

Re: [R-sig-phylo] Bipartition frequencies between two sets of trees

2012-08-27 Thread Klaus Schliep
Hi Alastair here is a solution, probably not the most elegant. You may look into the function as.splits, phangorn:::print.splits to improve the output and lento for a nicer way of plotting your results. x <- y <- list() for (i in 1:100) {x[[i]] <- rtree(20); y[[i]] <- rtree(20)} z = c(x,y) z = l

Re: [R-sig-phylo] problem with boot.phylo() and sample order randomisation

2012-07-08 Thread Klaus Schliep
Hi Alastair, I discovered two problems with the analysis. One is your data, which contains too many transitions and so you lost most of the information about your the process which generated the data. There is also a problem with prop.clades, which does not take care enough for different orderings

Re: [R-sig-phylo] R package for detecting positive selection?

2012-06-28 Thread Klaus Schliep
-phylo@r-project.org >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > -- > Emmanuel Paradis > IRD, Jakarta, Indonesia > http://ape.mpl.ird.fr/ > > ___ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] Cophenetic repeats

2012-05-27 Thread Klaus Schliep
Hello Ben, is your tree ultrametric? Do you have a e.g. UPGMA tree? This would explain your observation. You can test your tree with is.ultrametric(trx). Regards, Klaus On 5/27/12, Ben Weinstein wrote: > Hi all, > > I'm trying to decide if this an R error, or an error in > how I've implement

Re: [R-sig-phylo] center of tree

2012-05-22 Thread Klaus Schliep
-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] treefinder chronogram problems

2012-04-26 Thread Klaus Schliep
Hello John, it seems the chronogram contains the heights instead of the edge.lengths for each edge. Here is a small function to convert the tree. You should check if it is the same as in treefinder. convert.tree <- function(tree){ el = numeric(max(tree$edge)) el[tree$edge[,2]] = tree$edge.l

Re: [R-sig-phylo] tree comparison metrics in R

2012-04-13 Thread Klaus Schliep
; > 14 Taviton Street > > London WC1H 0BW > Tel: +44 (0) 2076798781 > > [[alternative HTML version deleted]] > > _______ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat

Re: [R-sig-phylo] parsimony bootstrapping

2012-04-06 Thread Klaus Schliep
Hi Brian, I just uploaded a new version of phangorn on CRAN (1.6-0) which solved the plotBS issue. The new version also returns silently a tree with the bootstrap values as node labels. So if you want to export a tree with edge length and bootstrap values, you should do something like this: treeR

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